Alexander J Petri @[email protected]

Doctoral Student in Computational Mathematics, Stockholms Universitet, SciLifeLab
Research focus: algorithms in bioinformatics

[Kristoffer Sahlin @krsahlin]

𝗣𝗼𝘀𝘁𝗱𝗼𝗰 𝗮𝗻𝗱 𝗣𝗵𝗗 𝗽𝗼𝘀𝗶𝘁𝗶𝗼𝗻𝘀 𝗶𝗻 𝗖𝗼𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 / 𝗔𝗹𝗴𝗼𝗿𝗶𝘁𝗵𝗺𝗶𝗰 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀

I am recruiting for both:

🔹 Postdoc position
https://t.co/sIjO7gXVU0

🔹 PhD position
https://t.co/zyw09ao7Qs

Please share!

[Kristoffer Sahlin @krsahlin]

1/ Our paper on Multi-Context Seeds is now out. We introduce a new seeding concept that improves read alignment accuracy while maintaining speed.
https://t.co/WMUURZ20Gy

[Jim Shaw @jim_elevator]

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler. With @lh3lh3.

https://t.co/ingqEXblza

[Kristoffer Sahlin @krsahlin]

@AlexanderJPetr1's isONclust3 algorithm is now published https://t.co/vl00fmyu9K. isONclust3 performs de novo clustering of long-read cDNA sequencing data. A key step in reference-free transcriptome analysis.

[Kristoffer Sahlin @krsahlin]

Strobealign v0.16.0 has been released. It comes with both runtime and accuracy improvements. Full changelog here https://t.co/79rwhSB3uX

[Kristoffer Sahlin @krsahlin]

As for my project (Project 1 in the list), please help spread the word to students interested in doing a PhD in Computational Biology/Bioinformatics. Note that PhD students here are employed with a salary, that the position comes with benefits, and that there are no tuition fees

[Kristoffer Sahlin @krsahlin]

We are hiring PhD students in Computational Mathematics and Mathematics at Stockholm University in various subjects:
https://t.co/s0SmOf8W5a

Application deadline: April 22 (1/3)

[Alexandru Tomescu @alextomescu.bsky.social @AlexTomescu0]

🚀Exciting PhD Opportunity🚀

Passionate about
🧬Graph algorithms for real-world genome sequencing?
💻Writing efficient, reusable code & libraries?
🌲Exploring stunning Nordic nature?

This PhD position is for YOU! 🎓✨

📅Apply by Mar 2
🔗https://t.co/DY2wog4qz8 #PhD #Algorithms

[Kristoffer Sahlin @krsahlin]

Strobealign v0.15.0 is released: (1) Allows more indexed contigs (2^32), (2) adds a mode --mcs which increase accuracy (paper on mcs https://t.co/6PUkIg2KFE). --mcs is still non-default in this release until we optimize it a bit more. Full changelog here https://t.co/cuKtpzsXLL

[bioRxiv Bioinfo @biorxiv_bioinfo]

De novo clustering of extensive long-read transcriptome datasets with isONclust3 https://t.co/qopsm9i0OC #biorxiv_bioinfo

[Alexander J Petri @[email protected] @AlexanderJPetr1]

@giulio_pibiri @ElenaMattei10 Congratulations!

[rustseq @rustseq]

Hello world! This is the official Twitter account for the rust-seq organization (https://t.co/C7JOr0MBKq). Follow us to learn more about rust-seq and the use of Rust in sequence bioinformatics!

[Giulio Ermanno Pibiri @giulio_pibiri]

I'd like to thank @nomad421, @curious_coding, @krsahlin, @AlexanderJPetr1, @daniel_c0deb0t, @mourisl, @ZarEskinCompMed, @MohsenZakeri1, Guillaume Marcais, Carl Kingsford (and all the others I'm forgetting rn) for all the nice chats we had. You made the experience really worthy!

[𝕐 @nomad421]

We had a great meeting & and are moving forward with a GitHub org. for planning & developing foundational building blocks for sequence analysis & related tasks in @rustlang. The org. "rust-seq" can be found here https://t.co/kZnN88se7f. Reach out if you're interested in joining!

[Sarahi L. Garcia @sarilog]

Are you looking for a postdoctoral researcher position?
There is an opening in my lab for a 5 year position to work on microbial interactions in aquatic environments
https://t.co/yifoQDop3e
Please RT

[Conesa Lab @Conesa_Lab]

We are looking for PhD Students and Postdocs to come join the @Conesa_Lab! DM if you are interested! Extra points if you can point out what is wrong with this picture! 😂

[Dr. Marta Tomaszkiewicz @amplicomics]

This work is finally out: https://t.co/DGMmfQtvll It started in 2019 when I designed short universal probes for capturing ampliconic gene transcripts from 9 gene families from 6 great apes. Two cDNA replicates per RNA sample, PacBio IsoSeq, clustering with isONclust by @krsahlin

[Alexander J Petri @[email protected] @AlexanderJPetr1]

@ThePhDPlace I'd be happy about one too

[Fairlie Reese / @fairlie.bsky.social @FairlieReese]

Happy to announce that Swan v3.0 (update fueled by thesis writing) is now available on GitHub and pip, with fully updated documentation! Check it out if you're interested in #longread RNA-seq analysis and visualization:

https://t.co/tgl6nan2yb
https://t.co/nksnFz5GPI

[Alexander J Petri @[email protected] @AlexanderJPetr1]

@kmlhpk Thank you. I am looking forward to meeting you at #ISMB

[Alexander J Petri @[email protected] @AlexanderJPetr1]

I am happy to share that our paper introducing isONform, a tool for de novo transcriptome recounstruction from Oxford Nanopore data, is now available in Bioinformatics https://t.co/uNagUovcrX and will be presented by me at #ISMB23 in Lyon.